US11959122B2 - Method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment - Google Patents

Method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment Download PDF

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US11959122B2
US11959122B2 US18/324,954 US202318324954A US11959122B2 US 11959122 B2 US11959122 B2 US 11959122B2 US 202318324954 A US202318324954 A US 202318324954A US 11959122 B2 US11959122 B2 US 11959122B2
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antibiotic
drug resistance
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antibiotics
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Xinyan Guo
Na Wang
Qingbin YUAN
Ni Ni
Xiaohui Zhang
Mali SHI
Jingbiao LI
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Nanjing University
Nanjing Institute of Environmental Sciences MEE
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  • the present disclosure relates to the technical field of water environment assessment, particularly to a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment.
  • Antibiotics refer to a class of secondary metabolites produced by microbes (including bacteria, fungi and Actinomyces ) or higher animals and plants in the course of life that have resistance to pathogens or other activities, and are chemical substances that can interfere with other cell development functions.
  • Antibiotics commonly used in clinic include extracts from microbial culture solutions and compounds synthesized or semi-synthesized through chemical methods.
  • Antibiotics play a role in treating infections by killing bacteria. As widely existing organisms, bacteria can also obtain resistance to antibiotics in various forms to escape the killing danger. This resistance is called “bacterial drug resistance”, and bacteria having drug resistance are called “drug-resistant bacteria”.
  • Ecological risk refers to the possibility of an ecosystem being affected by all factors except the ecosystem that pose a threat to the ecosystem, and refers to the potential effects of adverse effects such as chemical emissions, human activities and natural disasters on the ecosystem and its components within a certain area. These effects may lead to damage to the structure and function of the ecosystem, thereby endangering the safety and health of the ecosystem.
  • Patent CN109146242A discloses a dietary risk assessment method for antibiotic residues in aquaculture aquatic products, which belongs to the technical field of aquatic product quality and safety risk assessment.
  • original data is scored according to the grading table of each dietary risk influencing factor, and then brought into a mathematical model to obtain dietary risk scores.
  • the risk level is determined using score classification.
  • the present disclosure constructs an algorithm by through indicators such as aquaculture water environment, aquaculture organisms, antibiotic resistance, and aquatic product consumption for characterization and quick assessment of dietary risk levels.
  • Such the method is conducive to clarifying the monitoring priorities for the use of antibiotics in aquaculture in China in the future, and providing technical support for aquaculture farmers, fisheries regulatory authorities and others to manage the quality and safety of aquatic products.
  • the present disclosure provides a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment.
  • a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment comprising the following steps:
  • the target watershed includes a river basin, a sea area and a water functional area.
  • Microbial drug resistance high-level risk study assessment can be carried out on water environments such as rivers, oceans and watersheds.
  • the microbial flora in the step S 3 includes bacteria, fungi or Actinomyces , which are all typical microbes in water environments, and have certain representativeness.
  • the step S 3 further comprises environment persistence assessment: the half-life period t 1/2 of the target antibiotics or target antibiotic derivatives is obtained by database querying combined with model prediction, an environment persistence level is divided into 3 grades according to the size of the half-life period t 1/2 : non persistence is t 1/2 ⁇ 60d, persistence is 60d ⁇ t 1/2 ⁇ 180d, and high persistence is t 1/2 >180d; when t 1/2 >60, the target antibiotics or target antibiotic derivatives have environment persistence, so regardless of the drug resistance risk RQ R value of the microbial flora in the target watershed, step S 4 is carried out for further assessment. Combination of environment persistence with microbial drug resistance can make the assessment method more precise. When the target antibiotics or target antibiotic derivatives are not only persistent but also drug-resistant, it is needed to carry out high-level risk assessment. If the target antibiotics or target antibiotic derivatives are not persistent but drug-resistant, it is needed to timely carry out high-level risk assessment.
  • the pore diameter of the filter membrane in the step S 4 - 1 is 0.2-0.3 ⁇ m, which is beneficial to obtaining bacteria in water samples.
  • the phosphate buffer solution in the step S 4 - 1 and S 4 - 3 comprises 10 g/L of NaCl solution, 0.25 g/L of KCl solution, 1.6 g/L of Na2HPO4 solution, 0.3 g/L of KH2PO4 solution and the balance of water, and the pH of the phosphate buffer solution is 7.4.
  • This phosphate buffer solution is well compatible to bacteria.
  • the LB culture medium in the step S 4 - 1 comprises 10 g/L of tryptone, 5 g/L of yeast powder, 10 g/L of sodium chloride and the balance of water. This LB culture medium can effectively culture the bacteria.
  • step S 4 - 4 2-20 resistant genes are selected.
  • the dimensionless assessment factor AF is 10.
  • FIG. 1 is a flowchart of a method according to the present disclosure.
  • FIG. 2 is a diagram showing relative abundance and antibiotic drug-resistant gene concentration in experimental examples according to the present disclosure.
  • a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment comprises the following steps:
  • the target watershed was sea area.
  • the target watershed was a water function area, such as reservoir.
  • the target antibiotic was tetracycline.
  • a graph showing a corresponding relationship between the concentration of the obtained target antibiotic and the selectivity coefficient S is shown in FIG. 2 .
  • the average relative abundance P of the resistant gene was calculated by using the abundance of the target solution DNA of the target antibiotic. Specific parameters are seen in Table 1.
  • Parameter adjustments in examples 2-9 are all conventional adjustments in the present disclosure. Within the parameter variation range given in the present disclosure, all experimental parameters in examples 2-9 can achieve the assessment method of the present disclosure.
  • MIC Minimum inhibitory concentration of some antibiotics and drug resistance prediction invalid concentration (PNECr) of microbes
  • Antibiotics Resistant genes Aminoglycosides AC(1), AAC(2′), AAC(3), AAC(6′), ANT(2′′), ANT(3′′), ANT(4′), ANT(6), ANT(9), APH(2′′), APH(3′′), APH(3′), APH(4), APH(6), APH(7′′), and APH(9) ⁇ -lactams AER, BLA1, CTX-M, KPC, SHV, TEM, BlaB, CcrA, IMP, NDM, VIM, ACT, AmpC, CMY, LAT, PDC, OXA, blaI, blaR1, mecI, and mecR1 ⁇ -lactams CmlA, and cmxA Sulfonamides dfrA1, dfrA12, folA, sul1, sul2, sulA/folP, and sulA/folP Tetracyclines Tet(

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Abstract

A method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environments, belonging to the technical field of water environment assessment, comprises the following steps: S1, environment monitoring; S2, preliminary screening of antibiotics: S2-1, determination of n-octanol/water partition coefficient, and S2-2, determination of antibiotic environment concentration; S3, assessment of microbial drug resistance; and S4, high-level assessment. The assessment method of the present disclosure conducts a step-by-step assessment of target antibiotics or target antibiotic derivatives in water environment with risks.

Description

REFERENCE TO RELATED APPLICATIONS
The present application claims the priority of Chinese patent application No. 202210618679.5, filed on 2022 Jun. 1, the entire disclose of which is incorporated herein by reference.
TECHNICAL FIELD OF THE INVENTION
The present disclosure relates to the technical field of water environment assessment, particularly to a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment.
BACKGROUND OF THE INVENTION
Antibiotics refer to a class of secondary metabolites produced by microbes (including bacteria, fungi and Actinomyces) or higher animals and plants in the course of life that have resistance to pathogens or other activities, and are chemical substances that can interfere with other cell development functions. Antibiotics commonly used in clinic include extracts from microbial culture solutions and compounds synthesized or semi-synthesized through chemical methods.
Antibiotics play a role in treating infections by killing bacteria. As widely existing organisms, bacteria can also obtain resistance to antibiotics in various forms to escape the killing danger. This resistance is called “bacterial drug resistance”, and bacteria having drug resistance are called “drug-resistant bacteria”.
Ecological risk refers to the possibility of an ecosystem being affected by all factors except the ecosystem that pose a threat to the ecosystem, and refers to the potential effects of adverse effects such as chemical emissions, human activities and natural disasters on the ecosystem and its components within a certain area. These effects may lead to damage to the structure and function of the ecosystem, thereby endangering the safety and health of the ecosystem.
In people's production and daily life, risk is brought to water environments in various forms. However, there has been no suitable risk assessment method for ecological risk assessment of antibiotics in water environment. Patent CN109146242A discloses a dietary risk assessment method for antibiotic residues in aquaculture aquatic products, which belongs to the technical field of aquatic product quality and safety risk assessment. By establishing a group of dietary risk influencing factors and an assessment group of dietary risk levels, original data is scored according to the grading table of each dietary risk influencing factor, and then brought into a mathematical model to obtain dietary risk scores. The risk level is determined using score classification. The present disclosure constructs an algorithm by through indicators such as aquaculture water environment, aquaculture organisms, antibiotic resistance, and aquatic product consumption for characterization and quick assessment of dietary risk levels. Such the method is conducive to clarifying the monitoring priorities for the use of antibiotics in aquaculture in China in the future, and providing technical support for aquaculture farmers, fisheries regulatory authorities and others to manage the quality and safety of aquatic products.
However, no further research has been conducted on a relationship between antibiotic risk assessment and microbes.
SUMMARY OF THE INVENTION
For the above existing problems, the present disclosure provides a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment.
The technical solution of the present disclosure is as follows:
Provided is a method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment, comprising the following steps:
    • S1, environment monitoring:
    • S1-1: background survey on production, use and emission of antibiotics in a target watershed is carried out, a target antibiotic monitoring list is established for ecological risk assessment, and environment monitoring of target antibiotics is then carried out;
    • S1-2: target antibiotic derivative monitoring is carried out on the target watershed, a target antibiotic derivative monitoring list also needs to be established if byproduct reaction or biotransformation of target antibiotic occurs, and then environment monitoring of target antibiotics is carried out;
    • S2, preliminary screening of antibiotics: the target antibiotics of the target watershed obtained in step S1-1 and the target antibiotics of the target watershed obtained in step S1-2 are preliminarily screened, step S3 for microbial drug resistance assessment is carried out for further assessment if any one of S2-1 to S2-2 is met, or else the assessment is terminated;
    • S2-1, determination of n-octanol/water partition coefficient: the n-octanol/water partition coefficient Kow of the target antibiotic or target antibiotic derivative is calculated, and the logarithmic value of the obtained n-octanol/water partition coefficient Kow with a base of 10 is calculated, when 1 g Kow≥3.5, the target antibiotic or target antibiotic derivative has strong liposolubility, and then step S3 for microbial drug resistance assessment is carried out for further assessment;
    • S2-2, determination of antibiotic environment concentration: the environment concentration MEC of the target antibiotic or target antibiotic derivative is measured, the target antibiotic or target antibiotic derivative has a sustained input source when the environment concentration MEC≥10, and then step S3 for microbial drug resistance assessment is carried out for further assessment;
    • S3, microbial drug resistance assessment: the drug resistance risk of microbial flora in the target watershed is characterized by using drug resistance risk quotient value RQR, which is represented by the following formula:
      RQ R =MEC/PNEC R;
    • in the formula, MEC is the environment concentration of the target antibiotic or target antibiotic derivative measured in step S2-2, PNECR is a drug resistance prediction invalid concentration of microbial flora in the target watershed, which is represented by the following formula:
      PNEC R =MIC/AF;
    • in the formula, MIC is a minimum inhibitory concentration of microbial flora in the target watershed, AF is a dimensionless assessment factor, the minimum inhibitory concentration (MIC) of the microbial flora in the target watershed is determined through EUCAST database, thereby obtaining the drug resistance prediction invalid concentration (PNECR) of the microbial flora in the target watershed;
    • the drug resistance risk level of the microbial flora in the target watershed is divided into 4 grades according to the size of RQR value: no risk is RQR<0.01, low risk is 0.01<RQR<0.1, medium risk is 0.1<RQR<1 and high risk is RQR>1, the drug resistance risk level of the microbial flora in the target watershed is high when RQR>0.1, and then step S4 for high-level assessment is carried out for further assessment, or else the assessment is terminated;
    • S4, high-level assessment:
    • S4-1, extraction of environmental microbes: 50 weight parts of water samples in the target watershed are collected and then filtered through a filter membrane, the filter membrane is cut into fragments with an area of 15-28 mm2 after filtration, the fragments together with a phosphate buffer solution that is 1.2-1.5 times of the fragments in volume are put into a container, and then glass beads that are 2.5-3 times of the fragments in volume are added into the container, vortex oscillation is carried out for 15-20 min, and then the filter membrane and the glass beads are removed by filtration to obtain bacterial solution supernatant for later use;
    • S4-2, gradient concentration culture of antibiotics: the bacterial solution supernatant obtained in step S4-1 is respectively added into 5-6 sterilized conical flasks, 3 glass slides are put into each conical flask for stimulating biological membrane development of sediments, 0.2-0.5 weight part of LB culture medium is added, and then target antibiotics or target antibiotic derivatives with different concentrations that are 0, 0.01 μg/L, 0.1 μg/L, 1 μg/L, 10 μg/L and 100 μg/L respectively are added into the 5-6 different sterilized conical flasks, and then oscillatory reaction is carried out for 14 days at room temperature of 28-33° C. to obtain a target solution;
    • S4-3, DNA extraction: target solution DNA in the target solution obtained in step S4-2 is extracted while collecting bacteria on the glass slides in the sterilized conical flasks to the phosphate buffer solution to extract bacterial DNA;
    • S4-4, determination of resistant genes: resistant genes corresponding to the target antibiotics or target antibiotic derivatives are determined, the abundance of the target solution DNA or bacterial DNA is determined to calculate the average relative abundance P of the resistant gene, and meanwhile the average relative abundance P0 of the resistant gene before step S4 is calculated is calculated, and selectivity coefficient S is calculated, which is represented by the following formula:
      S=In(P/P 0)
    • S4-5, model fitting: antibiotic concentration C is taken as a horizontal ordinate, and the selectivity coefficient S corresponding to the target solution DNA or bacterial DNA is taken as a longitudinal ordinate, and fitting is carried out by using logistic model. When S=0, the corresponding antibiotic concentration C is the MSC value. The MSC values of the target solution DNA or bacterial DNA are compared, and the smaller MSC value is taken as control basis. This MSC value indicates that microbes carrying drug-resistant genes cannot be enriched under antibiotic conditions being higher than the antibiotic concentration C, so that the relative abundance of drug-resistant genes in the microbial flora is increased.
Further, the target watershed includes a river basin, a sea area and a water functional area. Microbial drug resistance high-level risk study assessment can be carried out on water environments such as rivers, oceans and watersheds.
Further, the microbial flora in the step S3 includes bacteria, fungi or Actinomyces, which are all typical microbes in water environments, and have certain representativeness.
Further, the step S3 further comprises environment persistence assessment: the half-life period t1/2 of the target antibiotics or target antibiotic derivatives is obtained by database querying combined with model prediction, an environment persistence level is divided into 3 grades according to the size of the half-life period t1/2: non persistence is t1/2<60d, persistence is 60d<t1/2<180d, and high persistence is t1/2>180d; when t1/2>60, the target antibiotics or target antibiotic derivatives have environment persistence, so regardless of the drug resistance risk RQR value of the microbial flora in the target watershed, step S4 is carried out for further assessment. Combination of environment persistence with microbial drug resistance can make the assessment method more precise. When the target antibiotics or target antibiotic derivatives are not only persistent but also drug-resistant, it is needed to carry out high-level risk assessment. If the target antibiotics or target antibiotic derivatives are not persistent but drug-resistant, it is needed to timely carry out high-level risk assessment.
Further, the pore diameter of the filter membrane in the step S4-1 is 0.2-0.3 μm, which is beneficial to obtaining bacteria in water samples.
Further, the phosphate buffer solution in the step S4-1 and S4-3 comprises 10 g/L of NaCl solution, 0.25 g/L of KCl solution, 1.6 g/L of Na2HPO4 solution, 0.3 g/L of KH2PO4 solution and the balance of water, and the pH of the phosphate buffer solution is 7.4. This phosphate buffer solution is well compatible to bacteria.
Further, the LB culture medium in the step S4-1 comprises 10 g/L of tryptone, 5 g/L of yeast powder, 10 g/L of sodium chloride and the balance of water. This LB culture medium can effectively culture the bacteria.
Further, in the step S4-4, 2-20 resistant genes are selected.
Further, in the step S3, the dimensionless assessment factor AF is 10.
The present disclosure has the beneficial effects:
    • (1) The a step-by-step assessment of target antibiotics or target antibiotic derivatives with risks is conducted by using the multi-level risk assessment method for microbial drug resistance of antibiotic residues in the water environment of the present disclosure. Firstly, the target antibiotics or target antibiotic derivatives are preliminarily screened, and the target antibiotics or target antibiotic derivatives are subjected to microbial drug resistance assessment for next-step assessment if meeting the conditions, and high-level risk assessment or assessment termination is continued to be carried out based on different drug resistances so as to finally obtain minimum inhibitory concentration (MSC) values which indicate that microbes carrying drug-resistant genes can be enriched under antibiotic conditions being higher than corresponding antibiotic concentration C so that the relative abundance of drug-resistant genes in microbial flora is increased.
    • (2) The multi-level risk assessment method for microbial drug resistance of antibiotic residues in the water environment of the present disclosure also combines environmental persistence with microbial drug resistance to make the assessment method more precise. If the target antibiotics or target antibiotic derivatives are not only persistent but also drug-resistant, high-risk assessment must be carried out. If the target antibiotics or target antibiotic derivatives are not persistent but resistant, high-level risk assessment is properly carried out.
    • (3) The multi-level risk assessment method for microbial drug resistance of antibiotic residues in the water environment of the present disclosure accurately measures the MSC value through experimental methods, with antibiotic concentration C as the horizontal ordinate and the selectivity coefficient S corresponding to the target solution DNA or bacterial DNA as the longitudinal ordinate. A logistic model is used for fitting to obtain the MSC value of the target solution DNA or bacterial DNA, and the smaller MSC value is taken as the control basis.
    • (4) The assessment results obtained by the multi-level risk assessment method for microbial drug resistance of antibiotic residues in water environment of the present disclosure play an important role in continuous monitoring, source analysis and source control of the water environment. Based on the assessment results, administrative measures such as investigation and rectification within a specified period can be adopted for pollution caused by point sources. For pollution caused by point sources, high ecological risk antibiotic types can be restricted or prohibited in relevant regions.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a flowchart of a method according to the present disclosure; and
FIG. 2 is a diagram showing relative abundance and antibiotic drug-resistant gene concentration in experimental examples according to the present disclosure.
 DETAILED DESCRIPTION Example 1
A method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment comprises the following steps:
    • S1, environment monitoring:
    • S1-1: background survey on production, use and emission of antibiotics in a target watershed was carried out, a target antibiotic monitoring list was established for ecological risk assessment, and environment monitoring of target antibiotics was then carried out;
    • S1-2: target antibiotic derivative monitoring was carried out on the target watershed, a target antibiotic derivative monitoring list also needed to be established if byproduct reaction or biotransformation of target antibiotic occurs, and then environment monitoring of target antibiotics was carried out;
    • S2, preliminary screening of antibiotics: the target antibiotics of the target watershed obtained in step S1-1 and the target antibiotics of the target watershed obtained in step S1-2 were preliminarily screened, step S3 for microbial drug resistance assessment was carried out if any one of S2-1 to S2-2 was met, or else the assessment was terminated;
    • S2-1, determination of n-octanol/water partition coefficient: the n-octanol/water partition coefficient Kow of the target antibiotic or target antibiotic derivative was calculated, and the logarithmic value of the obtained n-octanol/water partition coefficient Kow with a base of 10 was calculated, the target antibiotic or target antibiotic derivative was determined to have strong liposolubility when 1 g Kow≥3.5, and then step S3 for microbial drug resistance assessment was carried out for further assessment, as shown in appendix 1:
    • S2-2, determination of antibiotic environment concentration: the environment concentration MEC of the target antibiotic or target antibiotic derivative was measured, the target antibiotic or target antibiotic derivative had a sustained input source when the environment concentration MEC≥10, and then step S3 for microbial drug resistance assessment was carried out for further assessment;
    • S3, microbial drug resistance assessment: the drug resistance risk of microbial flora in the target watershed was characterized by using drug resistance risk quotient value RQR, which was represented by the following formula:
      RQ R =MEC/PNEC R;
    • in the formula, MEC was the environment concentration of the target antibiotic or target antibiotic derivative measured in step S2-2, PNECR was drug resistance prediction invalid concentration of microbial flora in the target watershed, which was represented by the following formula:
      PNEC R =MIC/AF;
    • in the formula, MIC was a minimum inhibitory concentration of microbial flora in the target watershed, AF was a dimensionless assessment factor which was 10, the minimum inhibitory concentration MIC of the microbial flora in the target watershed was determined by EUCAST database, thereby obtaining the drug resistance prediction invalid concentration PNECR of the microbial flora in the target watershed, as shown in appendix 2;
    • the drug resistance risk level of the microbial flora in the target watershed was divided into 4 grades according to the size of RQR value: no risk was RQR<0.01, low risk was 0.01<RQR<0.1, medium risk was 0.1<RQR<1 and high risk was RQR>1, the drug resistance risk level of the microbial flora in the target watershed was high when RQR>0.1, and then step S4 for high-level assessment was carried out for further assessment, or else the assessment was terminated;
    • S4, high-level assessment:
    • S4-1, extraction of environmental microbes: 50 weight parts of water samples in the target watershed were collected and then filtered through a filter membrane with a pore diameter of 0.25 μm, the filter membrane was cut into fragments with an area of 20 mm2 after filtration, the fragments together with a phosphate buffer solution that was 1.3 times of the fragments in volume were put into a container, wherein the phosphate buffer solution comprised 10 g/L of NaCl solution, 0.25 g/L of KCl solution, 1.6 g/L of Na2HPO4 solution, 0.3 g/L of KH2PO4 solution and the balance of water, the pH of the phosphate buffer solution was 7.4, and then glass beads that were 2.8 times of the fragments in volume were added into the container, vortex oscillation was carried out for 18 min, and then the filter membrane and the glass beads were removed by filtration to obtain bacterial solution supernatant for later use;
    • S4-2, gradient concentration culture of antibiotics: the bacterial solution supernatant obtained in step S4-1 was respectively added into 5 sterilized conical flasks, each sterilized conical flask contained 2.7 weight parts of bacterial solution supernatant, 3 glass slides were put into each conical flask for stimulating biological membrane development of sediments, 0.4 weight part of LB culture medium containing 10 g/L of tryptone, 5 g/L of yeast powder, 10 g/L of sodium chloride and the balance of water was added, and then target antibiotics or target antibiotic derivatives with different concentrations that were 0, 0.01 μg/L, 0.1 μg/L, 1 μg/L, 10 μg/L and 100 μg/L respectively were added into 5 different sterilized conical flasks, and then oscillatory reaction was carried out for 14 days at room temperature of 30° C. to obtain a target solution;
    • S4-3, DNA extraction: target solution DNA in the target solution obtained in step S4-2 was extracted while collecting bacteria on the glass slides in the sterilized conical flasks to the phosphate buffer solution to extract bacterial DNA;
    • S4-4, determination of resistant genes: resistant genes corresponding to the target antibiotics or target antibiotic derivatives were determined, 2-20 resistant genes were taken, and the maximum value was taken if there were less than 20, as shown in appendix 3. The abundance of the target solution DNA or bacterial DNA was determined to calculate the average relative abundance P of the resistant gene, and meanwhile the average relative abundance P0 of the resistant gene before step S4 was calculated, and selectivity coefficient S was calculated, which was represented by the following formula:
      S=In(P/P 0)
    • S4-5, model fitting: antibiotic concentration C was taken as a horizontal ordinate, and the selectivity coefficient S corresponding to the target solution DNA or bacterial DNA was taken as a longitudinal ordinate, and fitting was performed by using logistic model. When S=0, the corresponding antibiotic concentration C was the MSC value. The MSC values of the target solution DNA or bacterial DNA were compared, and the smaller MSC value was taken as control basis. This MSC value indicated that microbes carrying drug-resistant genes could not be enriched under antibiotic conditions being higher than the antibiotic concentration C, so that the relative abundance of drug-resistant genes in the microbial flora was increased.
Example 2
This example was different from example 1 in that:
The target watershed was sea area.
Example 3
This example was different from example 1 in that:
The target watershed was a water function area, such as reservoir.
Example 4
This example was different from example 1 in that:
    • the microbial flora in the step S3 was fungi.
Example 5
This example was different from example 1 in that:
    • the microbial flora in the step S3 was Actinomyces.
Example 7
This example was different from example 1 in that:
    • the step S3 further comprised environment persistence assessment: the half-life period t1/2 of the target antibiotics or target antibiotic derivatives was obtained by using database querying combined with model prediction, an environment persistence level was divided into 3 grades according to the size of the half-life period t1/2: non persistence was t1/2<60d, persistence was 60d<t1/2<180d, and high persistence was t1/2>180d; when t1/2>60, the target antibiotics or target antibiotic derivatives had environment persistence, so regardless of the drug resistance risk RQR value of the microbial flora in the target watershed, step S4 was carried out for further assessment, as shown in appendix 4.
Example 8
This example was different from example 1 in that:
    • S4-1, extraction of environmental microbes: 50 weight parts of water samples in the target watershed were collected and then filtered through a filter membrane with a pore diameter of 0.2 μm, the filter membrane was cut into fragments with an area of 15 mm2 after filtration, the fragments were put into a container and phosphate buffer solution that was 1.2 times of the fragments in volume was added, wherein the phosphate buffer solution comprised 10 g/L of NaCl solution, 0.25 g/L of KCl solution, 1.6 g/L of Na2HPO4 solution, 0.3 g/L of KH2PO4 solution and the balance of water, the pH of the phosphate buffer solution was 7.4, and then glass beads that were 2.5 times of the fragments in volume were added into the container, vortex oscillation was carried out for 15 min, and then the filter membrane and the glass beads were removed by filtration to obtain bacterial solution supernatant for later use;
    • S4-2, gradient concentration culture of antibiotics: the bacterial solution supernatant obtained in step S4-1 was respectively added into 6 sterilized conical flasks, each sterilized conical flask contained 2.5 weight parts of bacterial solution supernatant, 3 glass slides were put into each conical flask for stimulating biological membrane development of sediments, 0.2 weight part of LB culture medium containing 10 g/L of tryptone, 5 g/L of yeast powder, 10 g/L of sodium chloride and the balance of water was added, and then target antibiotics or target antibiotic derivatives with different concentrations that were 0, 0.01 μg/L, 0.1 μg/L, 1 μg/L, 10 μg/L and 100 μg/L respectively were added into 6 different sterilized conical flasks, and then oscillatory reaction was carried out for 14 days at room temperature of 28° C. to obtain a target solution.
Example 9
This example was different from example 1 in that:
    • S4-1, extraction of environmental microbes: 50 weight parts of water samples in the target watershed were collected and then filtered through a filter membrane with a pore diameter of 0.3 μm, the filter membrane was cut into fragments with an area of 28 mm2 after filtration, the fragments were put into a container and phosphate buffer solution that was 1.5 times of the fragments in volume is added, wherein the phosphate buffer solution comprised 10 g/L of NaCl solution, 0.25 g/L of KCl solution, 1.6 g/L of Na2HPO4 solution, 0.3 g/L of KH2PO4 solution and the balance of water, the pH of the phosphate buffer solution was 7.4, and then glass beads that were 3 times of the fragments in volume were added into the container, vortex oscillation was carried out for 20 min, and then the filter membrane and the glass beads were removed by filtration to obtain bacterial solution supernatant for later use;
    • S4-2, gradient concentration culture of antibiotics: the bacterial solution supernatant obtained in step S4-1 was respectively added into 6 sterilized conical flasks, each sterilized conical flask contained 3 weight parts of bacterial solution supernatant, 3 glass slides were put into each conical flask for stimulating biological membrane development of sediments, 0.5 weight part of LB culture medium containing 10 g/L of tryptone, 5 g/L of yeast powder, 10 g/L of sodium chloride and the balance of water was added, and then target antibiotics or target antibiotic derivatives with different concentrations that were 0, 0.01 μg/L, 0.1 μg/L, 1 μg/L, 10 μg/L and 100 μg/L respectively were added into 6 different sterilized conical flasks, and then oscillatory reaction was carried out for 14 days at room temperature of 33° C. to obtain a target solution.
Experimental Example
By taking method parameters in example 1 as an example, the target antibiotic was tetracycline. A graph showing a corresponding relationship between the concentration of the obtained target antibiotic and the selectivity coefficient S is shown in FIG. 2 . The average relative abundance P of the resistant gene was calculated by using the abundance of the target solution DNA of the target antibiotic. Specific parameters are seen in Table 1.
TABLE 1
Corresponding relationship between concentration and
selectivity coefficient of tetracycline
Example 1: tetracycline
Average relative Average relative
Concentration abundance P0 abundance P Selectivity
μg/L before experiment after experiment coefficient S
0.01 0.6 0.7 0.15
0.1 1 1.66 0.51
1 0.7 0.28 −0.91
10 0.5 0.4 −0.21
100 0.6 1.35 0.81
By combining FIG. 1 and FIG. 2 , it can be seen that the MSC value of the target antibiotic tetracycline, i.e., the corresponding antibiotic concentration at S=0 is about 3.3752=11.39 μg/L. Therefore, microbes carrying drug-resistant genes can be enriched under antibiotic conditions being higher than a tetracycline concentration of 11.39 μg/L. Parameter adjustments in examples 2-9 are all conventional adjustments in the present disclosure. Within the parameter variation range given in the present disclosure, all experimental parameters in examples 2-9 can achieve the assessment method of the present disclosure.
APPENDIX 1
Category Antibiotics log kow
Sulfonamides Acetylsulfonamide −0.604
Sulfamethazine 0.933
Sulfabenzamide 1.30
Sulfadimethoxazole 1.03
Sulfadiazine −0.090
Sulfamoxole 1.03
Sulfasalazine 0.350
Sulfachloropyridazine 0.310
Sulfamethoxydiazine 0.410
Sulfamethoxypyridazine 0.320
Quinolones Flumequine 1.60
Oxolinic acid 0.940
Enrofloxacin 0.700
Norfloxacin −1.03
Ofloxacin −0.39
Marbofloxacin −2.92
Cinoxacin 1.59
Ciprofloxacin −0.00080
Lomefloxacin 0.312
Fleroxacin 0.046
Pefloxacin −0.095
Macrolides Azithromycin 4.02
Roxithromycin 2.75
Erythromycin 3.06
Dehydrated erythromycin 4.34
Clarithromycin 3.16
Spiramycin 1.88
Tylosin 1.05
Lincomycins Clindamycin 2.16
Lincomycin 0.290
Tetracyclines Oxytetracycline −2.87
Tetracycline −1.33
Doxycycline −1.18
Lodermycin −1.14
Chlorquatrimycin 0.330
APPENDIX 2
Minimum inhibitory concentration (MIC) of some antibiotics and drug resistance prediction invalid concentration (PNECr) of microbes
Antibiotics Observed MIC PNECr
Amikacin 250 25
Amoxicillin 4 0.4
Amoxicillin-clavulanic acid (mixed at will) 1000 100
Amphotericin B 8 0.8
Ampicillin 4 0.4
Ampicillin-sulbactam sodium (mixed at will) 500 50
Ampicillin-sulbactam sodium (mixed in a ratio) 125 12.5
Anidurafenkin 2 0.2
Avilamycin 1000 100
Azithromycin 16 1.6
Aztreonam 32 3.2
Bacitracin 2000 200
Penicillin 4 0.4
Capreomycin 1000 100
Cefaclor 32 3.2
Cefadroxil 125 12.5
Cefalexin 250 25
Cefoperazone 2000 200
Cefoxitin 64 6.4
Cefazolin 32 3.2
Cefdinir 32 3.2
Cefepime 8 0.8
Clavulanic acid-cefepime proxetil 1000 100
Cefixime 4 0.4
Cefoperazone 16 1.6
Cefotaxime 2 0.2
Clavulanic acid-cefepime proxetil 8 0.8
Cefoxitin 250 25
Cefpirome 4 0.4
Cefpodoxime 8 0.8
Cefpodoxime-clavulanic acid 250 25
Ceftazidime 16 1.6
Clavulanic acid-ceftazidime 8 0.8
Ceftibuten 8 0.8
Ceftiofur 8 0.8
Ceftobiprole 4 0.4
Ceftriaxone 2 0.2
Cefuroxime 8 0.8
Chloramphenicol 125 12.5
Ciprofloxacin 2 0.2
Clarithromycin 8 0.8
Clarithromycin 32,000 3200
Clinafloxacin 32 3.2
Clindamycin 16 1.6
Cloxacillin 64 6.4
Colistin 64 6.4
Daptomycin 32 3.2
Doripenan 2 0.2
Doxycycline 32 3.2
Enrofloxacin 8 0.8
Ertapenem 2 0.2
Erythromycin 16 1.6
Ethambutol 1000 100
Faropenem 8 0.8
Fidaxomicin 8 0.8
FLORFENICOL 125 12.5
Fluconazol 64 6.4
Flumequine 64 6.4
Fosfomycin 125 12.5
Fusiform acid 32 3.2
Gatifloxacin 4 0.4
Difloxacin 2 0.2
Gentamicin 16 1.6
Imipenem 2 0.2
Isoniazide 64 6.4
Itraconazole 4 0.4
Kanamycin 125 12.5
Ketoconazole 4 0.4
Levofloxacin 4 0.4
Lincomycin 500 50
Linezolid 125 12.5
Lolakabiv 125 12.5
Messilinan 64 6.4
MeropeneM 2 0.2
Metronidazole 16 1.6
Mikafenjin 4 0.4
Minocycline 32 3.2
Moxifloxacin 2 0.2
Mupirocin 32 3.2
Nalidixic acid 500 50
Narasin 125 12.5
Neomycin 125 12.5
Netilmicin 16 1.6
Furantoin 4000 400
Norfloxacin 16 1.6
Ofloxacin 8 0.8
Oxacillin 32 3.2
Oxytetracycline 125 12.5
Pefloxacin 4000 400
Phenoxymethylpenicillin 4 0.4
Piperacillin 4 0.4
Piperacillin tazobactam 8 0.8
Quinupustine 4 0.4
Retapamulin 64 6.4
Rifampicin 8 0.8
Roxithromycin 2 0.2
Secnidazole 32 3.2
Sparfloxacin 500 50
Spectinomycin 2 0.2
Spiramycin 2000 200
Streptomycin 125 12.5
Sulbactam sodium 250 25
Sulfamethoxazole 1000 100
Teicoplanin 1000 100
Telithromycin 16 1.6
Tetracycline 16 1.6
Thiamphenicol 500 50
Tiamulin 500 50
Ticarcillin 250 25
Ticarcillin clavulanic acid 64 6.4
Tigecycline 16 1.6
Tilmicosin 250 25
Tobramycin 16 1.6
Trimethoprim 16 1.6
Trimethoprim sulfamethoxazole 8 0.8
Travafloxacin 8 0.8
Tylosin 2000 200
Vancomycin 125 12.5
Viomycin 1000 100
Virginiamycin 250 25
Voriconazole 2 0.2
APPENDIX 3
Types of resistant genes corresponding to antibiotics
Antibiotics Resistant genes
Aminoglycosides AC(1), AAC(2′), AAC(3),
AAC(6′), ANT(2″), ANT(3″),
ANT(4′), ANT(6), ANT(9),
APH(2″), APH(3″), APH(3′),
APH(4), APH(6), APH(7″), and
APH(9)
β-lactams AER, BLA1, CTX-M, KPC,
SHV, TEM, BlaB, CcrA, IMP,
NDM, VIM, ACT, AmpC,
CMY, LAT, PDC, OXA, blaI,
blaR1, mecI, and mecR1
β-lactams CmlA, and cmxA
Sulfonamides dfrA1, dfrA12, folA, sul1,
sul2, sulA/folP, and sulA/folP
Tetracyclines Tet(32), tet(34), tet(35),
tet(36), tet(37), tet(38), tetA,
tetB, tetC, tetD, tetE, tetG,
tetH, tetJ, tetK, tetL, tetM, tetO,
tetPA, tetPB, tetQ, tetR, tetS,
tetT, tetU, tetV, tetW, and tetX
Vancomycin vanA, vanB, vanC, vanC1,
vanG, vanHB, vanHD, vanRA,
vanRB, vanRC, vanRD,
vanSA, vanSB, vanSC, vanSE,
vanTC, vanTE, vanTG,
vanWB, vanWG, vanXA,
vanXB, anXD, vanYB, and
vanYD
Quinolones GyrA, GyrB, ParC, qnrA,
qnrB, qnrC, qnrS, qnrO, and
qnrW
Erythromycin, Lincomycin, and ereA, erm(34), erm(35),
streptomycin erm(36), ermA, ermA/ermTR,
ermB, ermC, ermF, ermJ/ermD,
ermK-01, ermT-01, ermT-02,
ermX, ermY, lmrA-01, lnuA-
01, lnuB-01, lnuB-02, lnuC,
matA/mel, mdtA, mefA,
mphA-01, mphA-02, mphB,
mphC, msrA-01, msrC-01,
oleC, pikR1, pikR2, vatB-01,
vatB-02, vatC-01, vatC-02,
vatD, vatE-01, vatE-02, vgaA-
01, vgaA-02, vgaB-01, vgaB-
02, vgb-01, vgbB-01, and
vgbB-02
APPENDIX 4
Half-life period of some antibiotics in water
Category Antibiotics t1/2 (h) Sources
Sulfonamides Sulfadiazine 9.00E+02 Literatures
Sulfamethazine 8.72E+02 Literatures
Acetylsulfonamide 9.00E+02 Literatures
Sulfamethoxazole 5.29E+02 Literatures
Sulfathiazole 9.12E+02 Literatures
Sulfachloropyridine 1.44E+03 Model calculation
Sulfamethoxydiazine 9.00E+02 Model calculation
Sulfamethizole 9.00E+02 Model calculation
Sulfamethazine 9.00E+02 Model calculation
Sulfabenzamide 9.00E+02 Model calculation
Sulfamethoxypyridazine 9.00E+02 Model calculation
Sulfadimoxine 9.00E+02 Model calculation
Sulfadimethoxypyrimidine 9.00E+02 Model calculation
Sulfadimethisoxazol 9.00E+02 Model calculation
Sulfamonomethoxine 9.00E+02 Model calculation
Sulphaguanidine 9.00E+02 Model calculation
Sulfaquinoxaline 9.00E+02 Model calculation
Trimethoprim 1.44E+03 Literatures
Quinolones Norfloxacin 1.44E+03 Model calculation
Ciprofloxacin 1.44E+03 Literatures
Ofloxacin 1.20E+02 Literatures
Lomefloxacin 4.32E+03 Model calculation
Enrofloxacin 4.32E+03 Literatures
Fleroxacin 4.32E+04 Model calculation
Pefloxacin 4.32E+03 Model calculation
Difloxacin 4.32E+04 Literatures
Marbofloxacin 1.44E+03 Model calculation
Enoxacin 4.32E+03 Model calculation
Macrolides Clarithromycin 4.32E+03 Model calculation
Spiramycin 4.32E+03 Model calculation
Azithromycin 4.32E+03 Model calculation
Spiramycin 4.32E+03 Model calculation
Erythromycin 4.32E+03 Model calculation
Roxithromycin 4.32E+03 Literatures
Tylosin 2.42E+03 Literatures
Dehydrated erythromycin 8.76E+03 Literatures
Lincomycins Lincomycin 9.00E+02 Model calculation
Clindamycin 1.44E+03 Model calculation
Tetracyclines Oxytetracycline 2.16E+02 Literatures
Tetracycline 7.20E+01 Literatures
Aureomycin 4.32E+03 Model calculation
Doxycycline 1.44E+03 Model calculation
Methacycline 1.44E+03 Model calculation
β-lactams Cefalexin 9.00E+02 Model calculation
Amoxicillin 9.00E+02 Model calculation
Penicillin 9.00E+02 Model calculation
Cefazolin 9.00E+02 Model calculation
Others Ormetoprim 1.44E+03 Model calculation
Florfenicol 1.44E+03 Model calculation
Chloramphenicol 1.44E+03 Model calculation
Armillarisin 1.44E+03 Model calculation

Claims (9)

The invention claimed is:
1. A method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment, comprising the following steps:
S1, environment monitoring:
S1-1: background survey on production, use and emission of antibiotics in a target watershed is carried out, a target antibiotic monitoring list is established for ecological risk assessment, and environment monitoring of target antibiotics is then carried out;
S1-2: target antibiotic derivative monitoring is carried out on the target watershed, a target antibiotic derivative monitoring list also needs to be established if byproduct reaction or biotransformation of target antibiotics occurs, and then environment monitoring of target antibiotic derivatives is carried out;
S2, preliminary screening of antibiotics: the target antibiotics of the target watershed obtained in step S1-1 and the target antibiotic derivatives of the target watershed obtained in step S1-2 are preliminarily screened, step S3 for microbial drug resistance assessment is carried out for further assessment if any one of S2-1 to S2-2 is met;
S2-1, determination of n-octanol/water partition coefficient: the n-octanol/water partition coefficient (Kow) of the target antibiotic or target antibiotic derivative is calculated, and the logarithmic value of the calculated n-octanol/water partition coefficient with a base of 10 is calculated, the target antibiotic or target antibiotic derivative has strong liposolubility when 1 g Kow≥3.5, and then step S3 for microbial drug resistance assessment is carried out for further assessment;
S2-2, determination of antibiotic environment concentration: the environment concentration (MEC) of the target antibiotic or target antibiotic derivative is measured, the target antibiotic or target antibiotic derivative has a sustained input source when MEC≥10, and then step S3 for microbial drug resistance assessment is carried out for further assessment;
S3, assessment of microbial drug resistance: the drug resistance risk of microbial flora in the target watershed is characterized by using drug resistance risk quotient value (RQr) which is represented by the following formula:

(RQr)=MEC/PNECr;
in the formula, MEC is the environment concentration of the target antibiotic or target antibiotic derivative measured in step S2-2, PNECr is a drug resistance prediction invalid concentration of microbial flora in the target watershed, which is represented by the following formula:

PNECr=MIC/AF;
in the formula, MIC is the minimum inhibitory concentration of microbial flora in the target watershed, AF is a dimensionless assessment factor, MIC of the microbial flora in the target watershed is determined by European Union Committee on Antimicrobial Susceptibility Testing (EUCAST) database, thereby obtaining PNECr of the microbial flora in the target watershed;
the drug resistance risk level of the microbial flora in the target watershed is divided into 4 grades according to the size of (RQr) value: no risk is (RQr)<0.01, low risk is 0.01<(RQr)<0.1, medium risk is 0.1<(RQr)<1 and high risk is (RQr)>1, the drug resistance risk level of the microbial flora in the target watershed is high when (RQr)>0.1, and then step S4 for high-level assessment is carried out for further assessment;
S4, high-level assessment:
S4-1, extraction of environmental microbes: 50 weight parts of water samples in the target watershed are collected and then filtered through a filter membrane, the filter membrane is cut into fragments with an area of 15-28 mm2 after filtration, the fragments together with a phosphate buffer solution that is 1.2-1.5 times of the fragments in volume are put into a container, and then glass beads that are 2.5-3 times of the fragments in volume are added into the container, vortex oscillation is carried out for 15-20 min, and then the filter membrane and the glass beads are removed by filtration to obtain bacterial solution supernatant for later use;
S4-2, gradient concentration culture of antibiotics: the bacterial solution supernatant obtained in step S4-1 is respectively added into 5-6 sterilized conical flasks, 3 glass slides are put into each conical flask for stimulating biological membrane development of sediments, 0.2-0.5 weight part of LB culture medium is added, and then target antibiotics or target antibiotic derivatives with different concentrations that are 0, 0.01 μg/L, 0.1 μg/L, 1 μg/L, 10 μg/L and 100 μg/L respectively are added into the 5-6 different sterilized conical flasks, and then oscillatory reaction is carried out for 14 days at room temperature of 28-33° C. to obtain a target solution;
S4-3, DNA extraction: DNA in the target solution obtained in step S4-2 is extracted while collecting bacteria on the glass slides in the sterilized conical flasks to the phosphate buffer solution to extract bacterial DNA;
S4-4, determination of resistant genes: resistant genes corresponding to the target antibiotics or target antibiotic derivatives are determined, the abundance of the target solution DNA or bacterial DNA is determined to calculate the average relative abundance (P) of the resistant genes, and meanwhile the average relative abundance P0 of the resistant genes before step S4 is calculated, and selectivity coefficient (S) is calculated, which is represented by the following formula:

S=In(P/P 0)
S4-5, model fitting: the antibiotic concentration (C or MSC) is taken as a horizontal ordinate, and the selectivity coefficient (S) corresponding to the target solution DNA or bacterial DNA is taken as a longitudinal ordinate, and fitting is carried out by using logistic model, when S=0, the corresponding antibiotic concentration is MSC value, the MSC values of the target solution DNA or bacterial DNA are compared, and the smaller MSC value is taken as control basis, the MSC value indicates that microbes carrying drug-resistant genes cannot be enriched under antibiotic conditions being higher than the antibiotic concentration, so that the relative abundance of drug-resistant genes in the microbial flora is increased.
2. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein the target watershed includes a river basin, a sea area and a reservoir.
3. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein the microbial flora in the step S3 includes bacteria, fungi or Actinomyces.
4. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein the step S3 further comprises environment persistence assessment: the half-life period t1/2 of the target antibiotics or target antibiotic derivatives is obtained by database querying combined with model prediction, an environment persistence level is divided into 3 grades according to the size of the half-life period t1/2: non persistence is t1/2<60d, persistence is 60d<t1/2<180d, and high persistence is t1/2>180d; when t1/2>60, the target antibiotics or target antibiotic derivatives have environment persistence, so regardless of the drug resistance risk RQr value of the microbial flora in the target watershed, step S4 is carried out for further assessment.
5. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein the pore diameter of the filter membrane in the step S4-1 is 0.2-0.3 μm.
6. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein the phosphate buffer solution in the step S4-4 and S4-3 comprises 10 g/L of NaCl solution, 0.25 g/L of KCl solution, 1.6 g/L of Na2HPO4 solution, 0.3 g/L of KH2PO4 solution and the balance of water, and the pH of the phosphate buffer solution is 7.4.
7. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein the LB culture medium in the step S4-1 comprises 10 g/L of tryptone, 5 g/L of yeast powder, 10 g/L of sodium chloride and the balance of water.
8. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein in the step S4-4, 2-20 resistant genes are selected.
9. The method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environment according to claim 1, wherein in the step S3, the dimensionless assessment factor (AF) is 10.
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